Variant report

Variant	rs12831221
Chromosome Location	chr12:4849359-4849360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10849118	0.82[CEU][hapmap]
rs11063307	1.00[ASN][1000 genomes]
rs12809178	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809919	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12816272	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817218	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821116	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827952	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16931649	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17701871	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs2286579	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34205979	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34214125	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34310347	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34337517	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34475613	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34502100	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34765166	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34947765	1.00[ASN][1000 genomes]
rs34952740	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35016874	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35288424	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35342320	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35464779	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35562639	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35715089	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35878255	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35899818	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35925396	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766273	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5007510	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55760751	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59096706	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59986414	1.00[ASN][1000 genomes]
rs66703365	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67871557	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68144469	1.00[ASN][1000 genomes]
rs71459918	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038876	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306593	1.00[ASN][1000 genomes]
rs960763	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1054218	chr12:4819576-4882667	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12831221	CD9	cis	parietal	SCAN
rs12831221	PRMT8	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4827400-4849600	Weak transcription	Fetal Brain Female	brain
2	chr12:4832200-4849800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr12:4832400-4849400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:4832600-4851600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:4834000-4870200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:4836400-4872400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:4837200-4853800	Weak transcription	Brain Germinal Matrix	brain
8	chr12:4842600-4852200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:4845000-4853800	Weak transcription	Fetal Brain Male	brain
10	chr12:4845000-4872600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:4847000-4855200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:4848600-4854600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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